Makefile.nongs

# ===========================================================================
#
#                            PUBLIC DOMAIN NOTICE
#               National Center for Biotechnology Information
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
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#
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#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
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#  Please cite the author in any work or product based on this material.
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# ===========================================================================

#setenv BOOST_PATH /netopt/ncbi_tools64/boost-1.62.0-ncbi1

ifdef BOOST_PATH
BOOST_INCL := -I $(BOOST_PATH)/include
BOOST_LIB := -L $(BOOST_PATH)/lib
endif


CC = c++ -std=c++11
CFLAGS = -D NO_NGS -Wall -Wno-format-y2k  -pthread -fPIC -O3 -finline-functions -fstrict-aliasing \
         -fomit-frame-pointer -msse4.2 $(BOOST_INCL)

PLATFORM=$(shell uname -s)

ifeq ($(PLATFORM),Linux)

LIBS = -Wl,-Bstatic $(BOOST_LIB) \
       -lboost_program_options \
       -lboost_iostreams \
       -lboost_regex \
       -lboost_timer \
       -lboost_chrono \
       -lboost_system \
       -Wl,-Bdynamic -lrt -ldl -lm  -lpthread -lz

else

LIBS = $(BOOST_LIB) \
       -lboost_program_options \
       -lboost_iostreams \
       -lboost_regex \
       -lboost_timer \
       -lboost_chrono \
       -lboost_system \
       -ldl -lm -lpthread -lz

endif

%.o: %.cpp
	$(CC) -c -o $@ $< $(CFLAGS)

binaries=skesa saute saute_prot gfa_connector kmercounter

all: $(binaries)

.PHONY: clean

clean: 
	rm -f $(binaries) *.o

glb_align.o: glb_align.hpp Makefile.nongs

skesa.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile.nongs
skesa: skesa.o glb_align.o
	$(CC) -o $@ $^ $(LIBS)

saute.o: guidedassembler.hpp guidedgraph.hpp gfa.hpp common_util.hpp guidedpath_naa.hpp readsgetter.hpp ngs_includes.hpp concurrenthash.hpp counter.hpp graphdigger.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile.nongs
saute: saute.o glb_align.o
	$(CC) -o $@ $^ $(LIBS)

saute_prot.o: guidedassembler.hpp guidedgraph.hpp genetic_code.hpp gfa.hpp common_util.hpp guidedpath_naa.hpp readsgetter.hpp ngs_includes.hpp concurrenthash.hpp counter.hpp graphdigger.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile.nongs
saute_prot: saute_prot.o glb_align.o
	$(CC) -o $@ $^ $(LIBS)

gfa_connector.o: gfa.hpp glb_align.hpp common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp graphdigger.hpp KmerInit.hpp  DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp Makefile.nongs
gfa_connector: gfa_connector.o glb_align.o
	$(CC) -o $@ $^ $(LIBS)

kmercounter.o: common_util.hpp concurrenthash.hpp readsgetter.hpp ngs_includes.hpp counter.hpp graphdigger.hpp assembler.hpp KmerInit.hpp DBGraph.hpp Integer.hpp LargeInt.hpp LargeInt1.hpp LargeInt2.hpp Model.hpp config.hpp glb_align.hpp Makefile.nongs
kmercounter: kmercounter.o glb_align.o
	$(CC) -o $@ $^ $(LIBS)